ESM-2
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence.
Overview
Protein foundation model evaluated by the PFMBench authors under their fine-tuning protocol. Input family: Sequence.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
Release 2026-09-17-134cd1815de8 · 12 evaluations · 12 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM-2 on PFMBench ANTI-RES: Antibiotic resistance Configuration: ESM-2Task: PFMBench ANTI-RES: Antibiotic resistanceDataset subset: Antibiotic resistance (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.63422 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Anti.Res.) Source checking is not independent reproduction. |
| ESM-2 on PFMBench BINDING-DB: BindingDB Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.13692 spearman Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Bind. DB) Source checking is not independent reproduction. |
| ESM-2 on PFMBench CLONING-CLF: Cloning CLF Configuration: ESM-2Task: PFMBench CLONING-CLF: Cloning CLFDataset subset: Cloning CLF (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.80586 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Clo. CLF) Source checking is not independent reproduction. |
| ESM-2 on PFMBench DEEPLOC2: DeepLoc2 Multi Configuration: ESM-2Task: PFMBench DEEPLOC2: DeepLoc2 MultiDataset subset: DeepLoc2 Multi (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0 .76191 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(DL2 M.) Source checking is not independent reproduction. |
| ESM-2 on PFMBench DEEPSOL: DeepSol Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.84494 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(DeepSol) Source checking is not independent reproduction. |
| ESM-2 on PFMBench EC: Enzyme Commission Configuration: ESM-2Task: PFMBench EC: Enzyme CommissionDataset subset: Enzyme Commission (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.73578 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(EC) Source checking is not independent reproduction. |
| ESM-2 on PFMBench MAT-PROD: Material production Configuration: ESM-2Task: PFMBench MAT-PROD: Material productionDataset subset: Material production (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.81189 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Mat.Pro.) Source checking is not independent reproduction. |
| ESM-2 on PFMBench METAL-ION: Metal ion binding Configuration: ESM-2Task: PFMBench METAL-ION: Metal ion bindingDataset subset: Metal ion binding (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.71170 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(M. I. Bin.) Source checking is not independent reproduction. |
| ESM-2 on PFMBench PDB-BIND: PDBbind Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.14677 spearman Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(PDBBind) Source checking is not independent reproduction. |
| ESM-2 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction Configuration: ESM-2Task: PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect predictionDataset subset: ProteinGym (PFMBench split) Scored zero-shot, with no fine-tuning, as reported in PFMBench Table 4. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.43904 spearman Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 4, row(ESM-2 [ 35 ]), column(ProteinGym) Source checking is not independent reproduction. |
| ESM-2 on PFMBench SEC-STRUCT: Secondary structure Configuration: ESM-2Task: PFMBench SEC-STRUCT: Secondary structureDataset subset: Secondary structure (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.76375 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Sec. Str.) Source checking is not independent reproduction. |
| ESM-2 on PFMBench STABILITY: TAPE_Stability Configuration: ESM-2Task: PFMBench STABILITY: TAPE_StabilityDataset subset: TAPE_Stability (PFMBench split) Fine-tuned with an adapter under the PFMBench harness; train, validation and test counts are in Table 1. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.32112 spearman Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedpfmbench primary benchmark evidence · Table 3, row(ESM-2 [ 35 ]), column(Stability) Source checking is not independent reproduction. |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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| Property and statement | Original source and location | Review and provenance |
|---|
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Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- pfmbench primary benchmark evidence · Original source · 2506.14796v1
Technical metadata and extraction receipts
Stable ID: pfmbench-method-esm-2
- areas
- proteins-complexes
- source locator
- Table 3, row(ESM-2 [ 35 ])
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: ESM-2 on PFMBench ANTI-RES: Antibiotic resistance
- model: ESM-2 on PFMBench BINDING-DB: BindingDB
- model: ESM-2 on PFMBench CLONING-CLF: Cloning CLF
- model: ESM-2 on PFMBench DEEPLOC2: DeepLoc2 Multi
- model: ESM-2 on PFMBench DEEPSOL: DeepSol
- model: ESM-2 on PFMBench EC: Enzyme Commission
- model: ESM-2 on PFMBench MAT-PROD: Material production
- model: ESM-2 on PFMBench METAL-ION: Metal ion binding
- model: ESM-2 on PFMBench PDB-BIND: PDBbind
- model: ESM-2 on PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction
- model: ESM-2 on PFMBench SEC-STRUCT: Secondary structure
- model: ESM-2 on PFMBench STABILITY: TAPE_Stability